Hybrid de novo Genome Assembly of Erwinia sp. E602 and Bioinformatic Analysis Characterized a New Plasmid-Borne lac Operon Under Positive Selection

Our previous study identified a new β-galactosidase in Erwinia sp. E602. To further understand the lactose metabolism in this strain, de novo genome assembly was conducted by using a strategy combining Illumina and PacBio sequencing technology. The whole genome of Erwinia sp. E602 includes a 4.8 Mb chromosome and a 326 kb large plasmid. A total of 4,739 genes, including 4,543 protein-coding genes, 25 rRNAs, 82 tRNAs and 7 other ncRNAs genes were annotated. The plasmid was the largest one characterized in genus Erwinia by far, and it contained a number of genes and pathways responsible for lactose metabolism and regulation. Moreover, a new plasmid-borne lac operon that lacked a typical β-galactoside transacetylase (lacA) gene was identified in the strain. Phylogenetic analysis showed that the genes lacY and lacZ in the operon were under positive selection, indicating the adaptation of lactose metabolism to the environment in Erwinia sp. E602. Our current study demonstrated that the hybrid de novo genome assembly using Illumina and PacBio sequencing technologies, as well as the metabolic pathway analysis, provided a useful strategy for better understanding of the evolution of undiscovered microbial species or strains.

Download Full-text

Improved hybrid de novo genome assembly and annotation of African wild rice, Oryza longistaminata , from Illumina and PacBio sequencing reads

The Plant Genome ◽

10.1002/tpg2.20001 ◽

2020 ◽

Vol 13 (1) ◽

Cited By ~ 1

Author(s):

Wei Li ◽

Kui Li ◽

Qun‐jie Zhang ◽

Ting Zhu ◽

Yun Zhang ◽

...

Keyword(s):

Genome Assembly ◽

Wild Rice ◽

De Novo ◽

Pacbio Sequencing ◽

De Novo Genome Assembly ◽

Oryza Longistaminata

Download Full-text

De Novo Sequencing and Hybrid Assembly of the Biofuel Crop Jatropha curcas L.: Identification of Quantitative Trait Loci for Geminivirus Resistance

Genes ◽

10.3390/genes10010069 ◽

2019 ◽

Vol 10 (1) ◽

pp. 69 ◽

Cited By ~ 9

Author(s):

Nagesh Kancharla ◽

Saakshi Jalali ◽

J. Narasimham ◽

Vinod Nair ◽

Vijay Yepuri ◽

...

Keyword(s):

Ssr Markers ◽

Genome Assembly ◽

Jatropha Curcas ◽

Quantitative Trait ◽

De Novo ◽

Mapping Population ◽

Single Copy ◽

Sequencing Data ◽

De Novo Genome Assembly ◽

Sequencing Technologies

Jatropha curcas is an important perennial, drought tolerant plant that has been identified as a potential biodiesel crop. We report here the hybrid de novo genome assembly of J. curcas generated using Illumina and PacBio sequencing technologies, and identification of quantitative loci for Jatropha Mosaic Virus (JMV) resistance. In this study, we generated scaffolds of 265.7 Mbp in length, which correspond to 84.8% of the gene space, using Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. Additionally, 96.4% of predicted protein-coding genes were captured in RNA sequencing data, which reconfirms the accuracy of the assembled genome. The genome was utilized to identify 12,103 dinucleotide simple sequence repeat (SSR) markers, which were exploited in genetic diversity analysis to identify genetically distinct lines. A total of 207 polymorphic SSR markers were employed to construct a genetic linkage map for JMV resistance, using an interspecific F2 mapping population involving susceptible J. curcas and resistant Jatropha integerrima as parents. Quantitative trait locus (QTL) analysis led to the identification of three minor QTLs for JMV resistance, and the same has been validated in an alternate F2 mapping population. These validated QTLs were utilized in marker-assisted breeding for JMV resistance. Comparative genomics of oil-producing genes across selected oil producing species revealed 27 conserved genes and 2986 orthologous protein clusters in Jatropha. This reference genome assembly gives an insight into the understanding of the complex genetic structure of Jatropha, and serves as source for the development of agronomically improved virus-resistant and oil-producing lines.

Download Full-text

Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma)

BMC Genomics ◽

10.1186/s12864-020-07042-7 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Pingping Liang ◽

Hafiz Sohaib Ahmed Saqib ◽

Xiaomin Ni ◽

Yingjia Shen

Keyword(s):

Dna Repair ◽

Positive Selection ◽

Single Molecule ◽

Genome Assembly ◽

De Novo ◽

Gene Families ◽

Comparative Genomic ◽

De Novo Genome Assembly ◽

Marine Medaka ◽

Oryzias Melastigma

Abstract Background Marine medaka (Oryzias melastigma) is considered as an important ecotoxicological indicator to study the biochemical, physiological and molecular responses of marine organisms towards increasing amount of pollutants in marine and estuarine waters. Results In this study, we reported a high-quality and accurate de novo genome assembly of marine medaka through the integration of single-molecule sequencing, Illumina paired-end sequencing, and 10X Genomics linked-reads. The 844.17 Mb assembly is estimated to cover more than 98% of the genome and is more continuous with fewer gaps and errors than the previous genome assembly. Comparison of O. melastigma with closely related species showed significant expansion of gene families associated with DNA repair and ATP-binding cassette (ABC) transporter pathways. We identified 274 genes that appear to be under significant positive selection and are involved in DNA repair, cellular transportation processes, conservation and stability of the genome. The positive selection of genes and the considerable expansion in gene numbers, especially related to stimulus responses provide strong supports for adaptations of O. melastigma under varying environmental stresses. Conclusions The highly contiguous marine medaka genome and comparative genomic analyses will increase our understanding of the underlying mechanisms related to its extraordinary adaptation capability, leading towards acceleration in the ongoing and future investigations in marine ecotoxicology.

Download Full-text

A Practical Comparison of De Novo Genome Assembly Software Tools for Next-Generation Sequencing Technologies

PLoS ONE ◽

10.1371/journal.pone.0017915 ◽

2011 ◽

Vol 6 (3) ◽

pp. e17915 ◽

Cited By ~ 144

Author(s):

Wenyu Zhang ◽

Jiajia Chen ◽

Yang Yang ◽

Yifei Tang ◽

Jing Shang ◽

...

Keyword(s):

Next Generation Sequencing ◽

Genome Assembly ◽

De Novo ◽

Software Tools ◽

Next Generation ◽

De Novo Genome Assembly ◽

Sequencing Technologies ◽

Generation Sequencing ◽

Assembly Software

Download Full-text

De novo Nanopore read quality improvement using deep learning

BMC Bioinformatics ◽

10.1186/s12859-019-3103-z ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 4

Author(s):

Nathan LaPierre ◽

Rob Egan ◽

Wei Wang ◽

Zhong Wang

Keyword(s):

Error Correction ◽

Genome Assembly ◽

Large Scale ◽

De Novo ◽

Error Rates ◽

De Novo Genome Assembly ◽

Sequencing Technologies ◽

Oxford Nanopore ◽

Long Read ◽

Read Error Correction

Abstract Background Long read sequencing technologies such as Oxford Nanopore can greatly decrease the complexity of de novo genome assembly and large structural variation identification. Currently Nanopore reads have high error rates, and the errors often cluster into low-quality segments within the reads. The limited sensitivity of existing read-based error correction methods can cause large-scale mis-assemblies in the assembled genomes, motivating further innovation in this area. Results Here we developed a Convolutional Neural Network (CNN) based method, called MiniScrub, for identification and subsequent “scrubbing” (removal) of low-quality Nanopore read segments to minimize their interference in downstream assembly process. MiniScrub first generates read-to-read overlaps via MiniMap2, then encodes the overlaps into images, and finally builds CNN models to predict low-quality segments. Applying MiniScrub to real world control datasets under several different parameters, we show that it robustly improves read quality, and improves read error correction in the metagenome setting. Compared to raw reads, de novo genome assembly with scrubbed reads produces many fewer mis-assemblies and large indel errors. Conclusions MiniScrub is able to robustly improve read quality of Oxford Nanopore reads, especially in the metagenome setting, making it useful for downstream applications such as de novo assembly. We propose MiniScrub as a tool for preprocessing Nanopore reads for downstream analyses. MiniScrub is open-source software and is available at https://bitbucket.org/berkeleylab/jgi-miniscrub.

Download Full-text

Human Genome Assembly in 100 Minutes

10.1101/705616 ◽

2019 ◽

Cited By ~ 20

Author(s):

Chen-Shan Chin ◽

Asif Khalak

Keyword(s):

Single Molecule ◽

Dna Sequences ◽

Genome Assembly ◽

De Novo ◽

Critical Factor ◽

Read Length ◽

De Novo Genome Assembly ◽

Small Indels ◽

Sequencing Technologies ◽

Long Read

AbstractDe novo genome assembly provides comprehensive, unbiased genomic information and makes it possible to gain insight into new DNA sequences not present in reference genomes. Many de novo human genomes have been published in the last few years, leveraging a combination of inexpensive short-read and single-molecule long-read technologies. As long-read DNA sequencers become more prevalent, the computational burden of generating assemblies persists as a critical factor. The most common approach to long-read assembly, using an overlap-layout-consensus (OLC) paradigm, requires all-to-all read comparisons, which quadratically scales in computational complexity with the number of reads. We assert that recently achievements in sequencing technology (i.e. with accuracy ~99% and read length ~10-15k) enables a fundamentally better strategy for OLC that is effectively linear rather than quadratic. Our genome assembly implementation, Peregrine uses sparse hierarchical minimizers (SHIMMER) to index reads thereby avoiding the need for an all-to-all read comparison step. Peregrine can assemble 30x human PacBio CCS read datasets in less than 30 CPU hours and around 100 wall-clock minutes to a high contiguity assembly (N50 > 20Mb). The continued advance of sequencing technologies coupled with the Peregrine assembler enables routine generation of human de novo assemblies. This will allow for population scale measurements of more comprehensive genomic variations -- beyond SNPs and small indels -- as well as novel applications requiring rapid access to de novo assemblies.

Download Full-text

Methods for De-novo Genome Assembly

10.20944/preprints202006.0324.v1 ◽

2020 ◽

Author(s):

Arash Bayat ◽

Hasindu Gamaarachchi ◽

Nandan P. Deshpande ◽

Marc R. Wilkins ◽

Sri Parameswaran

Keyword(s):

Genome Assembly ◽

De Novo ◽

Detailed Comparison ◽

Hybrid Assembly ◽

De Novo Genome Assembly ◽

Sequencing Technologies ◽

Oxford Nanopore ◽

Comparative Review ◽

Long Read ◽

Synthetic Datasets

Despite advances in algorithms and computational platforms, de-novo genome assembly remains a challenging process. Due to the constant innovation in sequencing technologies (Sanger, SOLiD, Illumina, 454, PacBio and Oxford Nanopore), genome assembly has evolved to respond to the changes in input data type. This paper includes a broad and comparative review of the most recent short-read, long-read and hybrid assembly techniques. In this review, we provide (1) an algorithmic description of the important processes in the workflow that introduces fundamental concepts and improvements; (2) a review of existing software that explains possible options for genome assembly; and (3) a comparison of the accuracy and the performance of existing methods executed on the same computer using the same processing capabilities and using the same set of real and synthetic datasets. Such evaluation allows a fair and precise comparison of accuracy in all aspects. As a result, this paper identifies both the strengths and weaknesses of each method. This comparative review is unique in providing a detailed comparison of a broad spectrum of cutting-edge algorithms and methods.

Download Full-text